ibb.test {ibb}R Documentation

The inverted beta-binomial test

Description

Performs the inverted beta-binomial test for paired count data.

Usage

ibb.test(x, tx, group, alternative = c("two.sided", "less", "greater"), n.threads = 1)

Arguments

x

A vector or matrix of counts. When x is a matrix, the test is performed row by row.

tx

A vector or matrix of the total sample counts. When tx is a matrix, the number of rows must be equal to the number of rows of x.

group

A vector of group indicators. There should be two groups of equal size. The samples are matched by the order of appearance in each group.

alternative

A character string specifying the alternative hypothesis: "two.sided" (default), "greater" or "less".

n.threads

The number of threads to be used.

Details

This test is designed for paired count data, for example data acquired before and after treatment.

Value

A list of values is returned:

p.value

The p-value of the test.

fc

An estimation of the common fold change.

Author(s)

Thang V. Pham

References

Pham TV, Jimenez CR (2012) An accurate paired sample test for count data. Bioinformatics, 28(18):i596-i602.

Examples

x <- c(33, 32, 86, 51, 52, 149)
tx <- c(7742608, 15581382, 20933491, 7126839, 13842297, 14760103)
group <- c(rep("cancer", 3), rep("normal", 3))
ibb.test(x, tx, group)

[Package ibb version 13.06 Index]